The game itself is split into three episodes, one for the player to command each race. In the first segment of the game, the player and Jim Raynor are attempting to control the colony of Mar Sara in the wake of the Zerg attacks on other Terran worlds.

The second campaign reveals that Kerrigan was not killed by the Zerg, but rather is captured and infested in an effort to incorporate her psionic traits into the Zerg gene pool.

The final episode of the game sees Aldaris and the Protoss government branding Tassadar a traitor and a heretic for conspiring with the dark templar. The player initially serves Aldaris in defending Aiur from the Zerg invasion, but while on a mission to arrest Tassadar, the player joins him instead.